diff --git a/packages/app-cli/tests/services/plugins/defaultPluginsUtils.ts b/packages/app-cli/tests/services/plugins/defaultPluginsUtils.ts
index 8508befc94..b661bc539c 100644
--- a/packages/app-cli/tests/services/plugins/defaultPluginsUtils.ts
+++ b/packages/app-cli/tests/services/plugins/defaultPluginsUtils.ts
@@ -1,11 +1,9 @@
-import { installDefaultPlugins, getDefaultPluginsInstallState, setSettingsForDefaultPlugins, checkPreInstalledDefaultPlugins } from '@joplin/lib/services/plugins/defaultPlugins/defaultPluginsUtils';
+import { afterDefaultPluginsLoaded, getDefaultPluginPathsAndSettings } from '@joplin/lib/services/plugins/defaultPlugins/defaultPluginsUtils';
 import PluginRunner from '../../../app/services/plugins/PluginRunner';
-import { pathExists } from 'fs-extra';
 import { checkThrow, setupDatabaseAndSynchronizer, supportDir, switchClient } from '@joplin/lib/testing/test-utils';
-import PluginService, { defaultPluginSetting, DefaultPluginsInfo, PluginSettings } from '@joplin/lib/services/plugins/PluginService';
+import PluginService, { defaultPluginSetting, DefaultPluginsInfo } from '@joplin/lib/services/plugins/PluginService';
 import Setting from '@joplin/lib/models/Setting';
 
-const testPluginDir = `${supportDir}/plugins`;
 
 function newPluginService(appVersion = '1.4') {
 	const runner = new PluginRunner();
@@ -27,13 +25,17 @@ function newPluginService(appVersion = '1.4') {
 describe('defaultPluginsUtils', () => {
 
 	const pluginsId = ['joplin.plugin.ambrt.backlinksToNote', 'org.joplinapp.plugins.ToggleSidebars'];
+	const defaultPluginsInfo = {
+		'joplin.plugin.ambrt.backlinksToNote': {},
+		'org.joplinapp.plugins.ToggleSidebars': {},
+	};
 
 	beforeEach(async () => {
 		await setupDatabaseAndSynchronizer(1);
 		await switchClient(1);
 	});
 
-	it('should install default plugins with no previous default plugins installed', (async () => {
+	it('should load default plugins when nor previously installed', (async () => {
 		const testPluginDir = `${supportDir}/pluginRepo/plugins`;
 		Setting.setValue('installedDefaultPlugins', []);
 
@@ -41,151 +43,69 @@ describe('defaultPluginsUtils', () => {
 
 		const pluginSettings = service.unserializePluginSettings(Setting.value('plugins.states'));
 
-		const newPluginsSettings = await installDefaultPlugins(service, testPluginDir, pluginsId, pluginSettings);
+		for (const pluginId of pluginsId) {
+			expect(pluginSettings[pluginId]).toBeFalsy();
+		}
 
-		const installedPluginPath1 = `${Setting.value('pluginDir')}/${pluginsId[0]}.jpl`;
-		const installedPluginPath2 = `${Setting.value('pluginDir')}/${pluginsId[1]}.jpl`;
-
-		expect(await pathExists(installedPluginPath1)).toBe(true);
-		expect(await pathExists(installedPluginPath2)).toBe(true);
-
-		expect(newPluginsSettings[pluginsId[0]]).toMatchObject(defaultPluginSetting());
-		expect(newPluginsSettings[pluginsId[1]]).toMatchObject(defaultPluginSetting());
+		const pluginPathsAndNewSettings = await getDefaultPluginPathsAndSettings(testPluginDir, defaultPluginsInfo, pluginSettings);
 
+		for (const pluginId of pluginsId) {
+			expect(
+				pluginPathsAndNewSettings.pluginSettings[pluginId],
+			).toMatchObject(defaultPluginSetting());
+		}
 	}));
 
-	it('should install default plugins with previous default plugins installed', (async () => {
-
+	it('should keep already created default plugins disabled with previous default plugins installed', (async () => {
 		const testPluginDir = `${supportDir}/pluginRepo/plugins`;
 		Setting.setValue('installedDefaultPlugins', ['org.joplinapp.plugins.ToggleSidebars']);
+		Setting.setValue('plugins.states', {
+			'org.joplinapp.plugins.ToggleSidebars': { ...defaultPluginSetting(), enabled: false },
+		});
 
 		const service = newPluginService('2.1');
 
 		const pluginSettings = service.unserializePluginSettings(Setting.value('plugins.states'));
+		const pluginPathsAndNewSettings = await getDefaultPluginPathsAndSettings(testPluginDir, defaultPluginsInfo, pluginSettings);
 
-		const newPluginsSettings = await installDefaultPlugins(service, testPluginDir, pluginsId, pluginSettings);
-
-		const installedPluginPath1 = `${Setting.value('pluginDir')}/${pluginsId[0]}.jpl`;
-		const installedPluginPath2 = `${Setting.value('pluginDir')}/${pluginsId[1]}.jpl`;
-
-		expect(await pathExists(installedPluginPath1)).toBe(true);
-		expect(await pathExists(installedPluginPath2)).toBe(false);
-
-		expect(newPluginsSettings[pluginsId[0]]).toMatchObject(defaultPluginSetting());
-		expect(newPluginsSettings[pluginsId[1]]).toBeUndefined();
+		// Should still be disabled
+		expect(
+			pluginPathsAndNewSettings.pluginSettings['org.joplinapp.plugins.ToggleSidebars'].enabled,
+		).toBe(false);
 	}));
 
-	it('should get default plugins install state', (async () => {
-		const testCases = [
-			{
-				'installedDefaultPlugins': [''],
-				'loadingPlugins': [`${testPluginDir}/simple`, `${testPluginDir}/jpl_test/org.joplinapp.FirstJplPlugin.jpl`],
-				'plugin1DefaultState': defaultPluginSetting(),
-				'plugin2DefaultState': defaultPluginSetting(),
-				'installedDefaultPlugins1': true,
-				'installedDefaultPlugins2': true,
-			},
-			{
-				'installedDefaultPlugins': [''],
-				'loadingPlugins': [`${testPluginDir}/simple`],
-				'plugin1DefaultState': defaultPluginSetting(),
-				'plugin2DefaultState': undefined,
-				'installedDefaultPlugins1': true,
-				'installedDefaultPlugins2': false,
-			},
-			{
-				'installedDefaultPlugins': ['org.joplinapp.plugins.Simple'],
-				'loadingPlugins': [`${testPluginDir}/simple`, `${testPluginDir}/jpl_test/org.joplinapp.FirstJplPlugin.jpl`],
-				'plugin1DefaultState': undefined,
-				'plugin2DefaultState': defaultPluginSetting(),
-				'installedDefaultPlugins1': true,
-				'installedDefaultPlugins2': true,
-			},
-			{
-				'installedDefaultPlugins': ['org.joplinapp.plugins.Simple'],
-				'loadingPlugins': [`${testPluginDir}/simple`],
-				'plugin1DefaultState': undefined,
-				'plugin2DefaultState': undefined,
-				'installedDefaultPlugins1': true,
-				'installedDefaultPlugins2': false,
-			},
-		];
-
-		for (const testCase of testCases) {
-			const service = newPluginService();
-			const pluginsId = ['org.joplinapp.plugins.Simple', 'org.joplinapp.FirstJplPlugin'];
-
-			Setting.setValue('installedDefaultPlugins', testCase.installedDefaultPlugins);
-			await service.loadAndRunPlugins(testCase.loadingPlugins, {});
-
-			// setting installedDefaultPlugins state
-			const defaultInstallStates: PluginSettings = getDefaultPluginsInstallState(service, pluginsId);
-
-			expect(defaultInstallStates[pluginsId[0]]).toStrictEqual(testCase.plugin1DefaultState);
-			expect(defaultInstallStates[pluginsId[1]]).toStrictEqual(testCase.plugin2DefaultState);
-
-
-			const installedDefaultPlugins = Setting.value('installedDefaultPlugins');
-			expect(installedDefaultPlugins.includes(pluginsId[0])).toBe(testCase.installedDefaultPlugins1);
-			expect(installedDefaultPlugins.includes(pluginsId[1])).toBe(testCase.installedDefaultPlugins2);
-
-		}
-
-	}));
-
-	it('should check pre-installed default plugins', (async () => {
-		// with previous pre-installed default plugins
-		Setting.setValue('installedDefaultPlugins', ['']);
-		let pluginSettings, installedDefaultPlugins;
-
-		pluginSettings = { [pluginsId[0]]: defaultPluginSetting() };
-		checkPreInstalledDefaultPlugins(pluginsId, pluginSettings);
-
-		installedDefaultPlugins = Setting.value('installedDefaultPlugins');
-		expect(installedDefaultPlugins.includes(pluginsId[0])).toBe(true);
-		expect(installedDefaultPlugins.includes(pluginsId[1])).toBe(false);
-
-
-		// with no previous pre-installed default plugins
-		Setting.setValue('installedDefaultPlugins', ['not-a-default-plugin']);
-		pluginSettings = {};
-		checkPreInstalledDefaultPlugins(pluginsId, pluginSettings);
-
-		installedDefaultPlugins = Setting.value('installedDefaultPlugins');
-		expect(installedDefaultPlugins.includes(pluginsId[0])).toBe(false);
-		expect(installedDefaultPlugins.includes(pluginsId[1])).toBe(false);
-
-	}));
+	const sampleJsBundlePlugin = `
+	/* joplin-manifest:
+	{
+		"id": "io.github.jackgruber.backup",
+		"manifest_version": 1,
+		"app_min_version": "1.4",
+		"name": "JS Bundle test",
+		"version": "1.0.0"
+	}
+	*/
+	joplin.plugins.register({
+		onStart: async function() {
+			await joplin.settings.registerSettings({
+				path: {
+					value: "initial-path",
+					type: 2,
+					section: "backupSection",
+					public: true,
+					label: "Backup path",
+				  },
+			})
+		},
+	});`;
 
 	it('should set initial settings for default plugins', async () => {
 		const service = newPluginService();
 
-		const pluginScript = `
-		/* joplin-manifest:
-		{
-			"id": "io.github.jackgruber.backup",
-			"manifest_version": 1,
-			"app_min_version": "1.4",
-			"name": "JS Bundle test",
-			"version": "1.0.0"
-		}
-		*/
-		joplin.plugins.register({
-			onStart: async function() {
-				await joplin.settings.registerSettings({
-					path: {
-						value: "initial-path",
-						type: 2,
-						section: "backupSection",
-						public: true,
-						label: "Backup path",
-					  },
-				})
-			},
-		});`;
 
-		const plugin = await service.loadPluginFromJsBundle('', pluginScript);
+		const plugin = await service.loadPluginFromJsBundle('', sampleJsBundlePlugin);
+		plugin.builtIn = true;
 		await service.runPlugin(plugin);
+		const runningPlugins = { 'io.github.jackgruber.backup': plugin };
 
 		const defaultPluginsInfo: DefaultPluginsInfo = {
 			'io.github.jackgruber.backup': {
@@ -199,46 +119,64 @@ describe('defaultPluginsUtils', () => {
 
 		// with pre-installed default plugin
 		Setting.setValue('installedDefaultPlugins', ['io.github.jackgruber.backup']);
-		setSettingsForDefaultPlugins(defaultPluginsInfo);
+		const pluginSettings = { 'io.github.jackgruber.backup': defaultPluginSetting() };
+
+		await afterDefaultPluginsLoaded(
+			runningPlugins,
+			defaultPluginsInfo,
+			pluginSettings,
+		);
 		expect(Setting.value('plugin-io.github.jackgruber.backup.path')).toBe('initial-path');
-		await service.destroy();
 
 		// with no pre-installed default plugin
 		Setting.setValue('installedDefaultPlugins', ['']);
-		setSettingsForDefaultPlugins(defaultPluginsInfo);
+		await afterDefaultPluginsLoaded(
+			runningPlugins,
+			defaultPluginsInfo,
+			pluginSettings,
+		);
 		expect(Setting.value('plugin-io.github.jackgruber.backup.path')).toBe(`${Setting.value('profileDir')}`);
 		await service.destroy();
 	});
 
+	it('should not overwrite existing settings for a user-installed version of a built-in plugin', async () => {
+		const service = newPluginService();
+
+		const plugin = await service.loadPluginFromJsBundle('', sampleJsBundlePlugin);
+		plugin.builtIn = false;
+		await service.runPlugin(plugin);
+
+		const defaultPluginsInfo: DefaultPluginsInfo = {
+			'io.github.jackgruber.backup': {
+				settings: {
+					'path': 'overwrite?',
+				},
+			},
+		};
+
+		// No pre-installed default plugins
+		Setting.setValue('installedDefaultPlugins', []);
+
+		// The plugin is running and enabled
+		const runningPlugins = { 'io.github.jackgruber.backup': plugin };
+		const pluginSettings = { 'io.github.jackgruber.backup': defaultPluginSetting() };
+
+		await afterDefaultPluginsLoaded(
+			runningPlugins,
+			defaultPluginsInfo,
+			pluginSettings,
+		);
+
+		// Should not overwrite
+		expect(Setting.value('plugin-io.github.jackgruber.backup.path')).toBe('initial-path');
+	});
+
 	it('should not throw error on missing setting key', async () => {
 
 		const service = newPluginService();
 
-		const pluginScript = `
-		/* joplin-manifest:
-		{
-			"id": "io.github.jackgruber.backup",
-			"manifest_version": 1,
-			"app_min_version": "1.4",
-			"name": "JS Bundle test",
-			"version": "1.0.0"
-		}
-		*/
-		joplin.plugins.register({
-			onStart: async function() {
-				await joplin.settings.registerSettings({
-					path: {
-						value: "initial-path",
-						type: 2,
-						section: "backupSection",
-						public: true,
-						label: "Backup path",
-					  },
-				})
-			},
-		});`;
-
-		const plugin = await service.loadPluginFromJsBundle('', pluginScript);
+		const plugin = await service.loadPluginFromJsBundle('', sampleJsBundlePlugin);
+		plugin.builtIn = true;
 		await service.runPlugin(plugin);
 
 		const defaultPluginsInfo: DefaultPluginsInfo = {
@@ -256,7 +194,10 @@ describe('defaultPluginsUtils', () => {
 		};
 
 		Setting.setValue('installedDefaultPlugins', ['']);
-		expect(checkThrow(() => setSettingsForDefaultPlugins(defaultPluginsInfo))).toBe(false);
+		const pluginSettings = { 'io.github.jackgruber.backup': defaultPluginSetting() };
+		const runningPlugins = { 'io.github.jackgruber.backup': plugin };
+
+		expect(checkThrow(() => afterDefaultPluginsLoaded(runningPlugins, defaultPluginsInfo, pluginSettings))).toBe(false);
 		expect(Setting.value('plugin-io.github.jackgruber.backup.path')).toBe(`${Setting.value('profileDir')}`);
 		await service.destroy();
 	});
diff --git a/packages/app-desktop/app.ts b/packages/app-desktop/app.ts
index 829a0431ed..267cce4fe9 100644
--- a/packages/app-desktop/app.ts
+++ b/packages/app-desktop/app.ts
@@ -65,7 +65,7 @@ import { AppState } from './app.reducer';
 import syncDebugLog from '@joplin/lib/services/synchronizer/syncDebugLog';
 import eventManager, { EventName } from '@joplin/lib/eventManager';
 import path = require('path');
-import { checkPreInstalledDefaultPlugins, installDefaultPlugins, setSettingsForDefaultPlugins } from '@joplin/lib/services/plugins/defaultPlugins/defaultPluginsUtils';
+import { afterDefaultPluginsLoaded, loadAndRunDefaultPlugins } from '@joplin/lib/services/plugins/defaultPlugins/defaultPluginsUtils';
 import userFetcher, { initializeUserFetcher } from '@joplin/lib/utils/userFetcher';
 import { parseNotesParent } from '@joplin/lib/reducer';
 import OcrService from '@joplin/lib/services/ocr/OcrService';
@@ -277,7 +277,6 @@ class Application extends BaseApplication {
 		const pluginRunner = new PluginRunner();
 		service.initialize(packageInfo.version, PlatformImplementation.instance(), pluginRunner, this.store());
 		service.isSafeMode = Setting.value('isSafeMode');
-		const defaultPluginsId = Object.keys(getDefaultPluginsInfo());
 
 		let pluginSettings = service.unserializePluginSettings(Setting.value('plugins.states'));
 		{
@@ -285,15 +284,11 @@ class Application extends BaseApplication {
 			// time, however we only effectively uninstall the plugin the next
 			// time the app is started. What plugin should be uninstalled is
 			// stored in the settings.
-			const newSettings = service.clearUpdateState(await service.uninstallPlugins(pluginSettings));
-			Setting.setValue('plugins.states', newSettings);
+			pluginSettings = service.clearUpdateState(await service.uninstallPlugins(pluginSettings));
+			Setting.setValue('plugins.states', pluginSettings);
 		}
 
-		checkPreInstalledDefaultPlugins(defaultPluginsId, pluginSettings);
-
 		try {
-			const defaultPluginsDir = path.join(bridge().buildDir(), 'defaultPlugins');
-			pluginSettings = await installDefaultPlugins(service, defaultPluginsDir, defaultPluginsId, pluginSettings);
 			if (await shim.fsDriver().exists(Setting.value('pluginDir'))) {
 				await service.loadAndRunPlugins(Setting.value('pluginDir'), pluginSettings);
 			}
@@ -302,19 +297,31 @@ class Application extends BaseApplication {
 		}
 
 		try {
+			const devPluginOptions = { devMode: true, builtIn: false };
+
 			if (Setting.value('plugins.devPluginPaths')) {
 				const paths = Setting.value('plugins.devPluginPaths').split(',').map((p: string) => p.trim());
-				await service.loadAndRunPlugins(paths, pluginSettings, true);
+				await service.loadAndRunPlugins(paths, pluginSettings, devPluginOptions);
 			}
 
 			// Also load dev plugins that have passed via command line arguments
 			if (Setting.value('startupDevPlugins')) {
-				await service.loadAndRunPlugins(Setting.value('startupDevPlugins'), pluginSettings, true);
+				await service.loadAndRunPlugins(Setting.value('startupDevPlugins'), pluginSettings, devPluginOptions);
 			}
 		} catch (error) {
 			this.logger().error(`There was an error loading plugins from ${Setting.value('plugins.devPluginPaths')}:`, error);
 		}
 
+		// Load default plugins after loading other plugins -- this allows users
+		// to override built-in plugins with development versions with the same
+		// ID.
+		const defaultPluginsDir = path.join(bridge().buildDir(), 'defaultPlugins');
+		try {
+			pluginSettings = await loadAndRunDefaultPlugins(service, defaultPluginsDir, getDefaultPluginsInfo(), pluginSettings);
+		} catch (error) {
+			this.logger().error(`There was an error loading plugins from ${defaultPluginsDir}:`, error);
+		}
+
 		{
 			// Users can potentially delete files from /plugins or even delete
 			// the complete folder. When that happens, we still have the plugin
@@ -322,7 +329,7 @@ class Application extends BaseApplication {
 			// out we remove from the state any plugin that has *not* been loaded
 			// above (meaning the file was missing).
 			// https://github.com/laurent22/joplin/issues/5253
-			const oldSettings = service.unserializePluginSettings(Setting.value('plugins.states'));
+			const oldSettings = pluginSettings;
 			const newSettings: PluginSettings = {};
 			for (const pluginId of Object.keys(oldSettings)) {
 				if (!service.pluginIds.includes(pluginId)) {
@@ -332,6 +339,7 @@ class Application extends BaseApplication {
 				newSettings[pluginId] = oldSettings[pluginId];
 			}
 			Setting.setValue('plugins.states', newSettings);
+			pluginSettings = newSettings;
 		}
 
 		this.checkAllPluginStartedIID_ = setInterval(() => {
@@ -346,7 +354,7 @@ class Application extends BaseApplication {
 				// tests to wait for plugins to load.
 				ipcRenderer.send('startup-plugins-loaded');
 
-				setSettingsForDefaultPlugins(getDefaultPluginsInfo());
+				void afterDefaultPluginsLoaded(service.plugins, getDefaultPluginsInfo(), pluginSettings);
 			}
 		}, 500);
 	}
diff --git a/packages/app-desktop/gui/ConfigScreen/ConfigScreen.tsx b/packages/app-desktop/gui/ConfigScreen/ConfigScreen.tsx
index 1ba1350ce3..bfb8eb455d 100644
--- a/packages/app-desktop/gui/ConfigScreen/ConfigScreen.tsx
+++ b/packages/app-desktop/gui/ConfigScreen/ConfigScreen.tsx
@@ -15,9 +15,6 @@ import SyncTargetRegistry from '@joplin/lib/SyncTargetRegistry';
 import * as shared from '@joplin/lib/components/shared/config/config-shared.js';
 import ClipperConfigScreen from '../ClipperConfigScreen';
 import restart from '../../services/restart';
-import PluginService from '@joplin/lib/services/plugins/PluginService';
-import { getDefaultPluginsInstallState, updateDefaultPluginsInstallState } from '@joplin/lib/services/plugins/defaultPlugins/defaultPluginsUtils';
-import getDefaultPluginsInfo from '@joplin/lib/services/plugins/defaultPlugins/desktopDefaultPluginsInfo';
 import JoplinCloudConfigScreen from '../JoplinCloudConfigScreen';
 import ToggleAdvancedSettingsButton from './controls/ToggleAdvancedSettingsButton';
 import shouldShowMissingPasswordWarning from '@joplin/lib/components/shared/config/shouldShowMissingPasswordWarning';
@@ -74,7 +71,6 @@ class ConfigScreenComponent extends React.Component<any, any> {
 				this.switchSection(this.props.defaultSection);
 			});
 		}
-		updateDefaultPluginsInstallState(getDefaultPluginsInstallState(PluginService.instance(), Object.keys(getDefaultPluginsInfo())), this);
 	}
 
 	private async handleSettingButton(key: string) {
diff --git a/packages/app-desktop/gui/ConfigScreen/controls/plugins/PluginBox.tsx b/packages/app-desktop/gui/ConfigScreen/controls/plugins/PluginBox.tsx
index bb257d6423..7cdab6379c 100644
--- a/packages/app-desktop/gui/ConfigScreen/controls/plugins/PluginBox.tsx
+++ b/packages/app-desktop/gui/ConfigScreen/controls/plugins/PluginBox.tsx
@@ -43,6 +43,7 @@ function manifestToItem(manifest: PluginManifest): PluginItem {
 		enabled: true,
 		deleted: false,
 		devMode: false,
+		builtIn: false,
 		hasBeenUpdated: false,
 	};
 }
@@ -52,6 +53,7 @@ export interface PluginItem {
 	enabled: boolean;
 	deleted: boolean;
 	devMode: boolean;
+	builtIn: boolean;
 	hasBeenUpdated: boolean;
 }
 
@@ -184,7 +186,10 @@ export default function(props: Props) {
 	}
 
 	function renderDeleteButton() {
+		// Built-in plugins can only be disabled
+		if (item.builtIn) return null;
 		if (!props.onDelete) return null;
+
 		return <Button level={ButtonLevel.Secondary} onClick={() => props.onDelete({ item })} title={_('Delete')}/>;
 	}
 
@@ -221,8 +226,7 @@ export default function(props: Props) {
 	}
 
 	const renderDefaultPluginLabel = () => {
-		// Built-in plugins can only be disabled
-		if (item.manifest._built_in) {
+		if (item.builtIn) {
 			return (
 				<BoxedLabel>{_('Built in')}</BoxedLabel>
 			);
diff --git a/packages/app-desktop/gui/ConfigScreen/controls/plugins/PluginsStates.tsx b/packages/app-desktop/gui/ConfigScreen/controls/plugins/PluginsStates.tsx
index edf907cffb..5023c5cb4c 100644
--- a/packages/app-desktop/gui/ConfigScreen/controls/plugins/PluginsStates.tsx
+++ b/packages/app-desktop/gui/ConfigScreen/controls/plugins/PluginsStates.tsx
@@ -81,6 +81,7 @@ function usePluginItems(plugins: Plugins, settings: PluginSettings): PluginItem[
 				enabled: setting.enabled,
 				deleted: setting.deleted,
 				devMode: plugin.devMode,
+				builtIn: plugin.builtIn,
 				hasBeenUpdated: setting.hasBeenUpdated,
 			});
 		}
@@ -149,8 +150,8 @@ export default function(props: Props) {
 		async function fetchPluginIds() {
 			// Built-in plugins can't be updated from the main repoApi
 			const nonDefaultPlugins = pluginItems
-				.map(p => p.manifest)
-				.filter(manifest => !manifest._built_in);
+				.filter(plugin => !plugin.builtIn)
+				.map(p => p.manifest);
 
 			const pluginIds = await repoApi().canBeUpdatedPlugins(nonDefaultPlugins, pluginService.appVersion);
 			if (cancelled) return;
@@ -288,8 +289,8 @@ export default function(props: Props) {
 				</UserPluginsRoot>
 			);
 		} else {
-			const nonDefaultPlugins = pluginItems.filter(item => !item.manifest._built_in);
-			const defaultPlugins = pluginItems.filter(item => item.manifest._built_in);
+			const nonDefaultPlugins = pluginItems.filter(item => !item.builtIn);
+			const defaultPlugins = pluginItems.filter(item => item.builtIn);
 			return (
 				<>
 					<UserPluginsRoot>
diff --git a/packages/default-plugins/buildDefaultPlugins.ts b/packages/default-plugins/buildDefaultPlugins.ts
index 0ccccca638..f1ac707c4a 100644
--- a/packages/default-plugins/buildDefaultPlugins.ts
+++ b/packages/default-plugins/buildDefaultPlugins.ts
@@ -1,7 +1,7 @@
 
 /* eslint-disable no-console */
 
-import { copy, exists, remove, mkdirp, readdir, mkdtemp, readFile, writeFile } from 'fs-extra';
+import { copy, exists, remove, mkdirp, readdir, mkdtemp } from 'fs-extra';
 import { join, resolve, basename } from 'path';
 import { tmpdir } from 'os';
 import { chdir, cwd } from 'process';
@@ -62,12 +62,6 @@ const buildDefaultPlugins = async (outputParentDir: string|null, beforeInstall:
 			logStatus('Initializing repository.');
 			await execCommand('git init . -b main');
 
-			logStatus('Marking manifest as built-in');
-			const manifestFile = './src/manifest.json';
-			const manifest = JSON.parse(await readFile(manifestFile, 'utf8'));
-			manifest._built_in = true;
-			await writeFile(manifestFile, JSON.stringify(manifest, undefined, '\t'));
-
 			logStatus('Creating initial commit.');
 			await execCommand('git add .');
 			await execCommand(['git', 'config', 'user.name', 'Build script']);
diff --git a/packages/lib/services/plugins/Plugin.ts b/packages/lib/services/plugins/Plugin.ts
index 4cbd572b67..1810eb602c 100644
--- a/packages/lib/services/plugins/Plugin.ts
+++ b/packages/lib/services/plugins/Plugin.ts
@@ -32,6 +32,7 @@ export default class Plugin {
 	private dispatch_: Function;
 	private eventEmitter_: any;
 	private devMode_ = false;
+	private builtIn_ = false;
 	// eslint-disable-next-line @typescript-eslint/ban-types -- Old code before rule was applied
 	private messageListener_: Function = null;
 	// eslint-disable-next-line @typescript-eslint/ban-types -- Old code before rule was applied
@@ -61,6 +62,14 @@ export default class Plugin {
 		this.devMode_ = v;
 	}
 
+	public get builtIn(): boolean {
+		return this.builtIn_;
+	}
+
+	public set builtIn(builtIn: boolean) {
+		this.builtIn_ = builtIn;
+	}
+
 	public get manifest(): PluginManifest {
 		return this.manifest_;
 	}
diff --git a/packages/lib/services/plugins/PluginService.ts b/packages/lib/services/plugins/PluginService.ts
index f6227b7f4f..8ef1de7a78 100644
--- a/packages/lib/services/plugins/PluginService.ts
+++ b/packages/lib/services/plugins/PluginService.ts
@@ -63,6 +63,11 @@ export interface PluginSettings {
 	[pluginId: string]: PluginSetting;
 }
 
+interface PluginLoadOptions {
+	devMode: boolean;
+	builtIn: boolean;
+}
+
 function makePluginId(source: string): string {
 	// https://www.npmjs.com/package/slug#options
 	return uslug(source).substr(0, 32);
@@ -340,7 +345,14 @@ export default class PluginService extends BaseService {
 		return this.runner_.callStatsSummary(pluginId, duration);
 	}
 
-	public async loadAndRunPlugins(pluginDirOrPaths: string | string[], settings: PluginSettings, devMode = false) {
+	public async loadAndRunPlugins(
+		pluginDirOrPaths: string | string[], settings: PluginSettings, options?: PluginLoadOptions,
+	) {
+		options ??= {
+			builtIn: false,
+			devMode: false,
+		};
+
 		let pluginPaths = [];
 
 		if (Array.isArray(pluginDirOrPaths)) {
@@ -370,6 +382,10 @@ export default class PluginService extends BaseService {
 				// such folders but to keep things sane we disallow it.
 				if (this.plugins_[plugin.id]) throw new Error(`There is already a plugin with this ID: ${plugin.id}`);
 
+				// We mark the plugin as built-in even if not enabled (being built-in affects
+				// update UI).
+				plugin.builtIn = options.builtIn;
+
 				this.setPluginAt(plugin.id, plugin);
 
 				if (!this.pluginEnabled(settings, plugin.id)) {
@@ -377,7 +393,7 @@ export default class PluginService extends BaseService {
 					continue;
 				}
 
-				plugin.devMode = devMode;
+				plugin.devMode = options.devMode;
 
 				await this.runPlugin(plugin);
 			} catch (error) {
diff --git a/packages/lib/services/plugins/defaultPlugins/defaultPluginsUtils.ts b/packages/lib/services/plugins/defaultPlugins/defaultPluginsUtils.ts
index 1e31428a0d..4b0837d084 100644
--- a/packages/lib/services/plugins/defaultPlugins/defaultPluginsUtils.ts
+++ b/packages/lib/services/plugins/defaultPlugins/defaultPluginsUtils.ts
@@ -1,90 +1,111 @@
 import produce from 'immer';
-import path = require('path');
 import Setting from '../../../models/Setting';
 import shim from '../../../shim';
-import PluginService, { defaultPluginSetting, DefaultPluginsInfo, PluginSettings } from '../PluginService';
+import PluginService, { defaultPluginSetting, DefaultPluginsInfo, Plugins, PluginSettings } from '../PluginService';
 import Logger from '@joplin/utils/Logger';
-import * as React from 'react';
-const shared = require('../../../components/shared/config/config-shared.js');
+import { join } from 'path';
 
 const logger = Logger.create('defaultPluginsUtils');
 
-export function checkPreInstalledDefaultPlugins(defaultPluginsId: string[], pluginSettings: PluginSettings) {
-	const installedDefaultPlugins: string[] = Setting.value('installedDefaultPlugins');
-	for (const pluginId of defaultPluginsId) {
-		// if pluginId is present in pluginSettings and not in installedDefaultPlugins array,
-		// then its either pre-installed by user or just uninstalled
-		if (pluginSettings[pluginId] && !installedDefaultPlugins.includes(pluginId)) Setting.setArrayValue('installedDefaultPlugins', pluginId);
-	}
-}
 
-export async function installDefaultPlugins(service: PluginService, defaultPluginsDir: string, defaultPluginsId: string[], pluginSettings: PluginSettings): Promise<PluginSettings> {
+// Use loadAndRunDefaultPlugins
+// Exported for testing.
+export const getDefaultPluginPathsAndSettings = async (
+	defaultPluginsDir: string, defaultPluginsInfo: DefaultPluginsInfo, pluginSettings: PluginSettings,
+) => {
+	const pluginPaths: string[] = [];
+
 	if (!await shim.fsDriver().exists(defaultPluginsDir)) {
 		logger.info(`Could not find default plugins' directory: ${defaultPluginsDir} - skipping installation.`);
-		return pluginSettings;
+		return { pluginPaths, pluginSettings };
 	}
+
 	const defaultPluginsPaths = await shim.fsDriver().readDirStats(defaultPluginsDir);
 	if (defaultPluginsPaths.length <= 0) {
-		logger.info(`Default plugins' directory is empty: ${defaultPluginsDir} - skipping installation.`);
-		return pluginSettings;
+		logger.info(`Default plugins' directory is empty: ${defaultPluginsDir} - no default plugins will be installed.`);
 	}
 
-	const installedPlugins = Setting.value('installedDefaultPlugins');
-
 	for (const pluginStat of defaultPluginsPaths) {
-		const pluginId = pluginStat.path;
+		// Each plugin should be within a folder with the same ID as the plugin
+		const pluginFolderName = pluginStat.path;
+		const pluginId = pluginFolderName;
 
-		// if pluginId is present in 'installedDefaultPlugins' array or it doesn't have default plugin ID, then we won't install it again as default plugin
-		if (installedPlugins.includes(pluginId) || !defaultPluginsId.includes(pluginId)) {
-			logger.debug(`Skipping default plugin ${pluginId}, ${!defaultPluginsId.includes(pluginId) ? '(Not a default)' : ''}`);
+		if (!defaultPluginsInfo.hasOwnProperty(pluginId)) {
+			logger.warn(`Default plugin ${pluginId} is missing in defaultPluginsInfo. Not loading.`);
 			continue;
 		}
-		const defaultPluginPath: string = path.join(defaultPluginsDir, pluginId, 'plugin.jpl');
-		await service.installPlugin(defaultPluginPath, false);
+
+		pluginPaths.push(join(defaultPluginsDir, pluginFolderName, 'plugin.jpl'));
 
 		pluginSettings = produce(pluginSettings, (draft: PluginSettings) => {
-			draft[pluginId] = defaultPluginSetting();
+			// Default plugins can be overridden but not uninstalled (as they're part of
+			// the app bundle). When overriding and unoverriding a default plugin, the plugin's
+			// state may be deleted.
+			// As such, we recreate the plugin state if necessary.
+			if (!draft[pluginId]) {
+				draft[pluginId] = defaultPluginSetting();
+			}
 		});
 	}
+
+	return { pluginSettings, pluginPaths };
+};
+
+export const loadAndRunDefaultPlugins = async (
+	service: PluginService,
+	defaultPluginsDir: string,
+	defaultPluginsInfo: DefaultPluginsInfo,
+	originalPluginSettings: PluginSettings,
+): Promise<PluginSettings> => {
+	const { pluginPaths, pluginSettings } = await getDefaultPluginPathsAndSettings(
+		defaultPluginsDir, defaultPluginsInfo, originalPluginSettings,
+	) ?? { pluginPaths: [], pluginSettings: originalPluginSettings };
+
+	await service.loadAndRunPlugins(pluginPaths, pluginSettings, { builtIn: true, devMode: false });
 	return pluginSettings;
-}
+};
 
-export function setSettingsForDefaultPlugins(defaultPluginsInfo: DefaultPluginsInfo) {
-	const installedDefaultPlugins = Setting.value('installedDefaultPlugins');
+// Applies setting overrides and marks default plugins as installed.
+// Should be called after plugins have finished loading.
+export const afterDefaultPluginsLoaded = async (
+	allLoadedPlugins: Plugins,
+	defaultPluginsInfo: DefaultPluginsInfo,
+	pluginSettings: PluginSettings,
+) => {
+	const installedDefaultPlugins: string[] = Setting.value('installedDefaultPlugins');
+	const allDefaultPlugins = Object.keys(defaultPluginsInfo);
 
-	// only set initial settings if the plugin is not present in installedDefaultPlugins array
-	for (const pluginId of Object.keys(defaultPluginsInfo)) {
-		if (!defaultPluginsInfo[pluginId].settings) continue;
-		for (const settingName of Object.keys(defaultPluginsInfo[pluginId].settings)) {
-			if (!installedDefaultPlugins.includes(pluginId) && Setting.keyExists(`plugin-${pluginId}.${settingName}`)) {
-				Setting.setValue(`plugin-${pluginId}.${settingName}`, defaultPluginsInfo[pluginId].settings[settingName]);
-			}
+	const isFirstLoadOfDefaultPlugin = (pluginId: string) => {
+		// Not installed?
+		if (!pluginSettings[pluginId]) {
+			return false;
 		}
-	}
-}
 
-export function getDefaultPluginsInstallState(service: PluginService, defaultPluginsId: string[]): PluginSettings {
-	const settings: PluginSettings = {};
-	for (const pluginId of defaultPluginsId) {
-		if (!service.pluginIds.includes(pluginId)) continue;
-		if (!Setting.setArrayValue('installedDefaultPlugins', pluginId)) {
-			settings[pluginId] = defaultPluginSetting();
+		// Not the first load
+		if (installedDefaultPlugins.includes(pluginId)) {
+			return false;
 		}
-	}
-	return settings;
-}
 
-export function updateDefaultPluginsInstallState(newPluginStates: PluginSettings, ConfigScreen: React.Component<any, any>) {
-	if (Object.keys(newPluginStates).length === 0) return;
-	const key = 'plugins.states';
-	const md = Setting.settingMetadata(key);
-	let newValue = Setting.value('plugins.states');
-	newValue = {
-		...newValue, ...newPluginStates,
+		// Return true only if the plugin is built-in (and not a user-installed
+		// copy).
+		//
+		// This avoids overriding existing user-set settings.
+		return allLoadedPlugins[pluginId]?.builtIn ?? false;
 	};
-	shared.updateSettingValue(ConfigScreen, key, newValue);
 
-	if (md.autoSave) {
-		shared.scheduleSaveSettings(ConfigScreen);
+	for (const pluginId of allDefaultPlugins) {
+		// if pluginId is present in pluginSettings and not in installedDefaultPlugins array,
+		// then it's a new default plugin and needs overrides applied.
+		if (isFirstLoadOfDefaultPlugin(pluginId)) {
+			// Postprocess: Apply setting overrides
+			for (const settingName of Object.keys(defaultPluginsInfo[pluginId].settings ?? {})) {
+				if (!installedDefaultPlugins.includes(pluginId) && Setting.keyExists(`plugin-${pluginId}.${settingName}`)) {
+					Setting.setValue(`plugin-${pluginId}.${settingName}`, defaultPluginsInfo[pluginId].settings[settingName]);
+				}
+			}
+
+			// Mark the plugin as installed so that postprocessing won't be done again.
+			Setting.setArrayValue('installedDefaultPlugins', pluginId);
+		}
 	}
-}
+};
diff --git a/packages/lib/services/plugins/utils/manifestFromObject.ts b/packages/lib/services/plugins/utils/manifestFromObject.ts
index ca58cf7311..e9231747cd 100644
--- a/packages/lib/services/plugins/utils/manifestFromObject.ts
+++ b/packages/lib/services/plugins/utils/manifestFromObject.ts
@@ -64,7 +64,6 @@ export default function manifestFromObject(o: any): PluginManifest {
 		icons: getIcons(),
 
 		_recommended: getBoolean('_recommended', false, false),
-		_built_in: getBoolean('_built_in', false, false),
 	};
 
 	validatePluginId(manifest.id);
diff --git a/packages/lib/services/plugins/utils/types.ts b/packages/lib/services/plugins/utils/types.ts
index e74d4db4a2..ef19341ae0 100644
--- a/packages/lib/services/plugins/utils/types.ts
+++ b/packages/lib/services/plugins/utils/types.ts
@@ -37,5 +37,4 @@ export interface PluginManifest {
 	_npm_package_name?: string;
 	_obsolete?: boolean;
 	_recommended?: boolean;
-	_built_in?: boolean;
 }
diff --git a/packages/plugin-repo-cli/lib/validateUntrustedManifest.ts b/packages/plugin-repo-cli/lib/validateUntrustedManifest.ts
index 2fd4004395..ffe5af79ee 100644
--- a/packages/plugin-repo-cli/lib/validateUntrustedManifest.ts
+++ b/packages/plugin-repo-cli/lib/validateUntrustedManifest.ts
@@ -13,16 +13,11 @@ const validateUntrustedManifest = (manifest: any, existingManifests: any) => {
 	validatePluginId(manifest.id);
 	validatePluginVersion(manifest.version);
 
-	// This prevents a plugin author from marking their own plugin as _recommended
-	// or _built_in.
+	// This prevents a plugin author from marking their own plugin as _recommended.
 	if (typeof manifest._recommended !== 'undefined') {
 		throw new Error(`Plugin ${manifest.id} cannot mark itself as recommended.`);
 	}
 
-	if (typeof manifest._built_in !== 'undefined') {
-		throw new Error(`Plugin ${manifest.id} cannot mark itself as built-in.`);
-	}
-
 	checkIfPluginCanBeAdded(existingManifests, manifest);
 };
 
diff --git a/readme/dev/spec/default_plugins.md b/readme/dev/spec/default_plugins.md
index e1fce59ec7..2fce2987cb 100644
--- a/readme/dev/spec/default_plugins.md
+++ b/readme/dev/spec/default_plugins.md
@@ -52,6 +52,7 @@ These are run by the `app-desktop` package on a full `build` (e.g. on `postinsta
 ## Installing of default plugins
 
 - All the functions related to default plugins are located in [defaultPluginsUtils.ts](https://github.com/laurent22/joplin/blob/eb7083d7888433ff6ef76ccfb7fb87ba951d513f/packages/lib/services/plugins/defaultPlugins/defaultPluginsUtils.ts)
-- On every startup, we check if there are new plugins available in build folder that have not been installed yet. After installing the new plugin, we update the `installedDefaultPlugins` array in `Setting.ts` with respective plugin ID for future reference.
-- After installing is complete, we apply the default settings for each default plugin. Default settings are located in [desktopDefaultPluginsInfo.ts](https://github.com/laurent22/joplin/blob/eb7083d7888433ff6ef76ccfb7fb87ba951d513f/packages/lib/services/plugins/defaultPlugins/desktopDefaultPluginsInfo.ts)
+- Default plugins are bundled with the app (included in the `build/` directory) and loaded from this directory.
+- To allow loading `dev` and NPM versions of the plugin, default plugins are loaded after non-default plugins. The plugin service refuses to load additional copies of already-loaded plugins. As such, non-default plugins take precedence over default plugins.
+- After loading is complete, we apply the default settings for each default plugin. Default settings are located in [desktopDefaultPluginsInfo.ts](https://github.com/laurent22/joplin/blob/eb7083d7888433ff6ef76ccfb7fb87ba951d513f/packages/lib/services/plugins/defaultPlugins/desktopDefaultPluginsInfo.ts). The `installedDefaultPlugins` setting is used to ensure that settnigs are only overridden once.
 - If the plugin is already installed by the user, then we don't apply default settings to avoid overriding user's settings.
\ No newline at end of file